Saccharomyces kudriavzevii
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Project description:Member of the Saccharomyces sensu lato budding yeast group
| PRJNA9593 | ENA
Project description:Saccharomyces sensu stricto budding yeast sequenced for comparative genomics studies of Saccharomyces species
| PRJNA9578 | ENA
Project description:Saccharomyces sensu stricto budding yeast used in winemaking and sequenced for comparative genomics studies
| PRJNA9577 | ENA
Project description:Saccharomyces sensu stricto budding yeast used in winemaking and sequenced for a comparative genomics study of Saccharomyces species
| PRJNA9589 | ENA
Project description:Transcriptional control of gene expression is a result of complex interactions between the cis-regulatory elements (CRE) at gene promoters. To understand the regulatory logic of a cell, we need to identify the CRE combinations that regulate gene expression. We developed a sensitive computational method to identify phylogenetically conserved CRE combinations for any species of interest. In contrast to previous methods, we do not need to align genomes to identify these combinations. We applied the method in 7 sensu stricto and sensu lato Saccharomyces species. 80% of the predictions displayed some evidence of combinatorial transcriptional behavior in several existing datasets including 1) ChIP-chip data for co-localization of transcription factors, 2) gene expression data for co-expression of predicted regulatory targets, and 3) gene ontology databases for common pathway membership of predicted regulatory targets. To establish definitive evidence that these CRE interactions influence TF occupancy, we performed ChIPseq experiments on transcription factors in a wild-type strain and strains in which a predicted cofactor was deleted. Our experiments showed that TF occupancy at the promoters of the CRE combination target genes depends on the predicted cofactor while occupancy of other promoters is independent of the predicted cofactor. ChIP-seq of 6 myc-tagged Transcription factors in wild-type and predicted co-factor knockout yeast strains in triplicate
2014-08-11 | E-GEOD-60281 | biostudies-arrayexpress
Project description:sensu stricto budding yeast ASlncRNA Transcriptome or Gene expression
| PRJNA278671 | ENA
Project description:RNAi, a gene-silencing pathway triggered by double-stranded RNA, is conserved in diverse eukaryotic species but has been lost in the model budding yeast, Saccharomyces cerevisiae. We report that RNAi is present in other budding-yeast species, including Saccharomyces castellii and Candida albicans. These species use noncanonical Dicer proteins to generate siRNAs, which mostly correspond to transposable elements and Y´ subtelomeric repeats. In S. castellii, RNAi mutants are viable but have excess Y´ mRNA levels. In S. cerevisiae, introducing Dicer and Argonaute of S. castellii restores RNAi, and the reconstituted pathway silences endogenous retrotransposons. These results identify a novel class of Dicer proteins, bring the tool of RNAi to the study of budding yeasts, and bring the tools of budding yeast to the study of RNAi.
2009-09-10 | GSE17870 | GEO
Project description:Transcriptional control of gene expression is a result of complex interactions between the cis-regulatory elements (CRE) at gene promoters. To understand the regulatory logic of a cell, we need to identify the CRE combinations that regulate gene expression. We developed a sensitive computational method to identify phylogenetically conserved CRE combinations for any species of interest. In contrast to previous methods, we do not need to align genomes to identify these combinations. We applied the method in 7 sensu stricto and sensu lato Saccharomyces species. 80% of the predictions displayed some evidence of combinatorial transcriptional behavior in several existing datasets including 1) ChIP-chip data for co-localization of transcription factors, 2) gene expression data for co-expression of predicted regulatory targets, and 3) gene ontology databases for common pathway membership of predicted regulatory targets. To establish definitive evidence that these CRE interactions influence TF occupancy, we performed ChIPseq experiments on transcription factors in a wild-type strain and strains in which a predicted cofactor was deleted. Our experiments showed that TF occupancy at the promoters of the CRE combination target genes depends on the predicted cofactor while occupancy of other promoters is independent of the predicted cofactor.
2014-08-11 | GSE60281 | GEO
Project description:The budding yeast Saccharomyces cerevisiae is a popular host to be used to produce recombinant proteins. Here we studied three yeast strains with different productivity using the RNA-seq data to elucidate the mechanisms for improving protein production.
2020-10-26 | GSE147204 | GEO
Project description:Short-read RNA-seq was performed on rRNA-depleted RNA isolated from spores of the budding yeast Saccharomyces cerevisiae that were sorted by mating type.
2021-08-17 | GSE180221 | GEO